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-rw-r--r--gn/packages/bioinformatics.scm75
1 files changed, 73 insertions, 2 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 58110a7..5fdbd4d 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -1584,7 +1584,8 @@ multiple sequence alignment.")
(base32 "1qcjhd4wcajik71z5347fw2sfhfkv0p6y7yldrrkmycw2qhqmpzn"))))
(build-system gnu-build-system)
(arguments
- `(#:tests? #f ; fix later
+ `(#:test-target "test"
+ #:parallel-tests? #f ; not supported
#:phases
(modify-phases %standard-phases
(delete 'configure) ; There is no configure phase.
@@ -1626,6 +1627,75 @@ multiple sequence alignment.")
(("\\.\\./trash") "/var/cache/genome"))
#t)))
+
+ (add-before 'check 'pre-check
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out"))
+ (triplet ,(gnu-triplet->nix-system (%current-system))))
+ (setenv "PATH" (string-append (getenv "PATH")
+ ":" out "/bin"))
+ (setenv "MACHTYPE"
+ (string-take triplet (string-index triplet #\-)))
+ (for-each make-file-writable
+ (find-files "utils/bedJoinTabOffset/tests"))
+ (substitute* '("utils/bamToPsl/tests/makefile"
+ "utils/trackDbIndexBb/tests/makefile")
+ (("/cluster/bin/bedtools/bedtools") (which "bedtools")))
+
+ ;; These tests fail intermittently:
+ (substitute* "utils/vcfFilter/tests/makefile"
+ ((" testRenameNoGt ") " ")
+ ((" testMinAc1NoGt ") " "))
+
+ ;; These tests can't find their database:
+ (substitute* "hg/lib/tests/makefile"
+ ((" spDbTest ") " ")
+ ((" hdbTest ") " "))
+ (substitute* "hg/lib/tests/genePredTests.mk"
+ ((" tableTests ") " ")
+ ((" compatTblTests ") " "))
+ (substitute* "hg/lib/tests/pslReaderTests.mk"
+ ((" tableTests") " "))
+ (substitute* "hg/lib/tests/makefile"
+ ((" annoGratorTest ") " ")
+ ((" customTrackTest ") " ")
+ ((" hgvsTest") " "))
+ (substitute* "hg/autoSql/tests/makefile"
+ ((" dbLinkTest ") " ")
+ ((" symColsTest ") " "))
+ (delete-file "hg/checkTableCoords/tests/makefile")
+ (delete-file "hg/hgGetAnn/tests/makefile")
+ (substitute* "hg/sqlToXml/makefile"
+ ((".*doTest.*") ""))
+ (substitute* "hg/utils/genePredFilter/tests/makefile"
+ ((" gencodeHackDbTest") " "))
+ (substitute* "hg/utils/refSeqGet/tests/makefile"
+ (("^test::.*") "test:: mkout\n"))
+ (delete-file "hg/utils/vcfToHgvs/tests/makefile")
+ (substitute* "hg/bedItemOverlapCount/tests/makefile"
+ ((".*RunTest.*") ""))
+
+ ;; Depends on /cluster
+ (substitute* "hg/liftOver/tests/makefile"
+ (("^test:.*") "test: mkdirs scaffoldEndBug\n"))
+ (delete-file "hg/mouseStuff/netToAxt/tests/makefile")
+ (substitute* "hg/pslToChain/tests/makefile"
+ ((" example1 ") " "))
+
+ ;; Depends on /gbdb
+ (delete-file "hg/mouseStuff/chainBridge/tests/makefile")
+
+ ;; Depends on /hive
+ (delete-file "hg/utils/genePredToProt/tests/makefile")
+
+ ;; Unclear why this fails
+ (delete-file "hg/utils/hgvsToVcf/tests/makefile")
+
+ ;; Wants network
+ (substitute* "hg/utils/hubCheck/tests/makefile"
+ (("^test::.*") "test:: one two\n"))
+ #t)))
+
;; Install happens during the 'build phase.
;; Install the website files too
(replace 'install
@@ -1658,7 +1728,8 @@ multiple sequence alignment.")
("python2" ,python-2)
("zlib" ,zlib)))
(native-inputs
- `(("gs-fonts" ,gs-fonts)
+ `(("bedtools" ,bedtools)
+ ("gs-fonts" ,gs-fonts)
("pkg-config" ,pkg-config)
("python" ,python)
("rsync" ,rsync) ; For installing js files from the source checkout